I feel really stupid not being able to figure this out and have extensively googled this. Surprisingly not one person has wondered this or just figured it out right away..
How do you send mod4/super/windows key through chicken of the vnc. There are shortcuts for crtl alt del equivalents and stuff but not mod4 ? I feel dumb.
I'm using Chicken, which is the successor to Chicken of the VNC, but I had the same issue. This is what I figured out. To enable the command key to send as Mod4, go to:
Connection > Connection Profiles > Modifiers
Then set the dropdown option for "Command" to "Windows" (i.e., the "Windows" key, which Linux recognizes as Mod4/Superkey).
Hope this helps.